MDM RNA-seq Analysis Report
Note
RNAseq data from Adam Fields’ Laboratory, University of California San Diego (UCSD).
Summary
Number of samples: 2Groups: HIV- moderate cannabis, HIV- daily cannabis, HIV- naive to cannabis, HIV+ naive to cannabis, HIV+ daily cannabis, HIV+ moderate cannabisTreatments: CBD, CBDpIL1B, IL1B, THC, THCpIL1B, VehicleHIV status: HIVn, HIVpCannabis use: moderate, daily, naive
Workflow Overview
We processed the RNA-seq data from monocyte-derived macrophages (MDMs) using the following pipeline:
DESeq2 Model
The differential expression model used:
\[ design(dds) ~ treatment + HIV status + cannabis \]
treatment: vehicle, IL1b, CBD, THC, CBD+IL1B, THC+IL1b
hiv_status: HIV- vs HIV+
cannabis: naive, moderate, daily
Summary Analyses
Volcano Plots
volcano_list[["cannabis_daily_vs_naive"]]PCA Plots
using ntop=500 top features by variance
using ntop=500 top features by variance
using ntop=500 top features by variance
using ntop=500 top features by variance
Top Genes Tables
DT::datatable(top20_list[["cannabis_daily_vs_naive"]], options = list(pageLength = 5, scrollX = TRUE), rownames = FALSE)
Note
- Only genes with padj < 0.05 and |log2FC| > 1 are labeled in volcano plots.
- PCA plots can be faceted by
hiv_statusto observe group separation.
- Interactive tables allow scrolling and sorting top genes for each contrast.
HIV × Cannabis Interaction Analysis in MDMs
Methods
We computed per-donor log2 fold changes (log2FC) for each treatment contrast:
\[ \text{log2FC} = \log_2(\text{Treatment} + 1) - \log_2(\text{Control} + 1) \]
Contrasts included:
IL1B vs Vehicle
CBD+IL1B vs IL1B
THC+IL1B vs IL1B
Known inflammatory genes were highlighted to assess whether cannabis dampens IL1β-induced inflammation. For each gene and contrast, we fitted a linear model:
Next, we extracted the interaction terms to test whether cannabis use modulates IL1β-induced inflammation.
Top HIV × Cannabis interaction genes (ordered by raw p-value)
CBD and THC Modulation of IL1β Response (Key Inflammatory Genes)
- Grey points: all other genes — context for overall variation.
- Colored points + labels: known inflammatory genes (IL6, TNF, CXCL10, CCL2, NFKB1).
- Y-axis (log2FC): positive → increased by cannabinoid, negative → decreased (potential dampening).
- Black points and error bars: mean ± SD of inflammatory genes per cannabis group and HIV status.
- Observation:
- Most inflammatory genes are near 0, suggesting minimal average dampening by CBD or THC.
- Some genes show donor-specific shifts, indicating variability among donors.